Related Experiment Video
Updated: May 25, 2026
13:30
A New Screening Method for the Directed Evolution of Thermostable Bacteriolytic Enzymes
Published on: November 7, 2012
Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates
Ruiqi Huang1, Frank Hippauf, Diana Rohrbeck
1Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA.
Summary
Ancestral protein resurrection reveals that latent ancestral enzyme activities can be enhanced and co-opted into preferred functions through gene duplication and positive selection, driving protein evolution.
Area of Science:
- Evolutionary biology
- Biochemistry
- Molecular genetics
Background:
- Protein evolution involves functional shifts, but the role of ancestral variation is debated.
- Gene duplication provides raw material for new protein functions.
- Understanding how ancestral states influence evolutionary trajectories is crucial.
Purpose of the Study:
- To investigate the role of ancestral functional variation in generating protein functional shifts.
- To examine the evolutionary mechanisms driving changes in enzyme activity and substrate specificity.
- To explore how latent ancestral activities are co-opted over evolutionary time.
Main Methods:
- Ancestral protein resurrection and functional assays.
- Statistical tests for positive selection.
- Forward and reverse evolutionary genetics, including mutagenesis studies.
- Analysis of enzyme kinetics (k(cat)/K(M)) for competing substrates.
Main Results:
- Demonstrated improvement of ancestral nonpreferred activities in daughter enzymes post-gene duplication.
- Provided evidence that functional shifts were coincident with positive selection.
- Validated the impact of specific amino acid sites on enhancing activity with ancestral nonpreferred substrates.
- Documented an evolutionary reversal of an active site residue altering enzyme properties.
- Showed that adaptive substitutions affect substrate discrimination and enzyme kinetics (k(cat)/K(M)) separately.
Conclusions:
- Latent or nonpreferred ancestral protein activities can be co-opted to become primary functions.
- Positive selection and gene duplication are key drivers of functional innovation in enzymes.
- Specific amino acid replacements significantly influence substrate specificity and catalytic efficiency during evolution.
Related Concept Videos
01:07Catalytically Perfect Enzymes
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
01:13Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
01:13Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
02:34Enzymes
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
01:24Evolution of New Traits in Microbes
Microorganisms evolve rapidly due to their large population sizes and short generation times, often exhibiting measurable changes within days under laboratory conditions. Natural selection acts on standing genetic variation, enabling the retention and amplification of beneficial traits that confer fitness advantages in changing environments.Adaptive Pigment Regulation in RhodobacterIn Rhodobacter, a genus of purple non-sulfur bacteria, light-harvesting pigments such as bacteriochlorophyll and...
01:22Introduction to Enzymes
The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that bind the substrates and convert them into products. Many enzymes also...